If the modules are the same there is no reason why the qualifications should be any less valued by employers.
I would think in many cases the modules won't be the same, though.
It would be a logistical nightmare for a university to try to deliver 2 and 3 year programmes simultaneously in STEM subjects for which linear progression through modules is essential.
A student on the 3 year course would take 4 modules in 2 semesters, each year.
A student on the 2 year course would need to take 12 modules in each year. So the first half of the year 2 modules would have to delivered in the summer session, then the second half of year 2 in the Autumn semester, the first half of year 3 in the Spring semester and the second half of year 3 in the Summer semester. The last three would be out of phase with the 3 year programme, meaning that modules would either have to delivered several times per year (very expensive), or you would have to drop the requirement linear progression through modules (which would be quite difficult for many key modules in STEM subjects).
As I and other academics wrote above, it would seem more likely that research intensive universities stick principally to 3 year courses with other (private) institutions specialising in 2 year courses in particular subjects.